Added one data

Author: nuwang

lib/galaxy/dependencies/__init__.py

@@ -238,6 +238,9 @@ def check_fs_googledrivefs(self):
     def check_fs_gcsfs(self):
         return 'googlecloudstorage' in self.file_sources
 
+    def check_fs_onedatafs(self):
+        return 'onedata' in self.file_sources
+
     def check_watchdog(self):
         install_set = {'auto', 'True', 'true', 'polling', True}
         return (self.config['watch_tools'] in install_set

lib/galaxy/dependencies/conditional-requirements.txt

@@ -22,6 +22,7 @@ s3fs  # type: s3fs
 fs.anvilfs # type: anvil
 fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
+fs-onedatafs # type: onedata
 
 # Chronos client
 chronos-python==1.2.1

lib/galaxy/files/sources/onedata.py

@@ -0,0 +1,20 @@
+try:
+    from fs.onedatafs import OnedataFS
+except ImportError:
+    OnedataFS = None
+
+from ._pyfilesystem2 import PyFilesystem2FilesSource
+
+
+class OneDataFilesSource(PyFilesystem2FilesSource):
+    plugin_type = 'onedata'
+    required_module = OnedataFS
+    required_package = "fs-onedatafs"
+
+    def _open_fs(self, user_context):
+        props = self._serialization_props(user_context)
+        handle = OnedataFS(**props)
+        return handle
+
+
+__all__ = ('OneDataFilesSource',)

test/unit/files/_util.py

@@ -60,7 +60,9 @@ def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, i
             'googledrive|client_id': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID'),
             'googledrive|client_secret': os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET'),
             'googlecloudstorage|project': os.environ.get('GALAXY_TEST_GCS_PROJECT'),
-            'googlecloudstorage|bucket_name': 'genomics-public-data'
+            'googlecloudstorage|bucket_name': 'genomics-public-data',
+            'onedata|provider_host': os.environ.get('GALAXY_TEST_ONEDATA_PROVIDER_HOST'),
+            'onedata|access_token': os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
         },
         role_names=role_names or set(),
         group_names=group_names or set(),

test/unit/files/onedata_file_sources_conf.yml

@@ -0,0 +1,5 @@
+- type: onedata
+  id: test1
+  doc: Test access to a OneData host
+  provider_host: ${user.preferences['onedata|provider_host']}
+  access_token: ${user.preferences['onedata|access_token']}

test/unit/files/test_googledrive.py

@@ -13,10 +13,10 @@
 
 skip_if_no_google_drive_access_token = pytest.mark.skipif(
     not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN')
-    and os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN')
-    and os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID')
-    and os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET'),
-    reason="GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN not set"
+    and not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN')
+    and not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID')
+    and not os.environ.get('GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET'),
+    reason="GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN and related vars not set"
 )
 
 

test/unit/files/test_onedata.py

@@ -0,0 +1,38 @@
+import os
+
+import pytest
+
+from galaxy.files import ConfiguredFileSources, ConfiguredFileSourcesConfig
+from ._util import (
+    assert_realizes_as,
+    find_file_a,
+    user_context_fixture,
+)
+SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
+FILE_SOURCES_CONF = os.path.join(SCRIPT_DIRECTORY, "onedata_file_sources_conf.yml")
+
+skip_if_no_onedata_access_token = pytest.mark.skipif(
+    not os.environ.get('GALAXY_TEST_ONEDATA_PROVIDER_HOST')
+    and not os.environ.get('GALAXY_TEST_ONEDATA_ACCESS_TOKEN'),
+    reason="GALAXY_TEST_ONEDATA_PROVIDER_HOST and GALAXY_TEST_ONEDATA_ACCESS_TOKEN not set"
+)
+
+
+@skip_if_no_onedata_access_token
+def test_file_source():
+    user_context = user_context_fixture()
+    file_sources = _configured_file_sources()
+    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")
+
+    assert file_source_pair.path == "/"
+    file_source = file_source_pair.file_source
+    res = file_source.list("/", recursive=False, user_context=user_context)
+    a_file = find_file_a(res)
+    assert a_file
+
+    assert_realizes_as(file_sources, "gxfiles://test1/a", "a\n", user_context=user_context)
+
+
+def _configured_file_sources(conf_file=FILE_SOURCES_CONF):
+    file_sources_config = ConfiguredFileSourcesConfig()
+    return ConfiguredFileSources(file_sources_config, conf_file=conf_file)